Household Robots Do Not Protect Users' Security And Privacy, Researchers Say

Robots equipped with wireless and sensing capabilities are available for use in the home. But the safety and privacy risks of these devices are not yet adequately addressed, according to a new study.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 12:00 pm

First 'One-way Roads' For Light Could Lead To Simpler Lightwave Technology

Light readily bounces off obstacles in its path. Some of these reflections are captured by our eyes, thus participating in the visual perception of the objects around us. In contrast to this usual behavior of light, researchers have implemented for the first time a one-way structure in which microwave light flows losslessly around obstacles or defects. This concept, when used in lightwave circuits, might one day reduce their internal connections to simple one-way conduits with much improved capacity and efficiency.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 12:00 pm

Rare Head And Neck Cancer Linked To HPV, Study Finds

An increase in cases of a rare type of head and neck cancer appears to be linked to HPV, or human papillomavirus, according to a new study.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 12:00 pm

Future Diabetes Treatment May Use Resveratrol To Target The Brain

A new study shows that the brain plays a key role in mediating resveratrol's anti-diabetic actions, potentially paving the way for future orally delivered diabetes medications that target the brain.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 12:00 pm

Bacterium Transforms Toxic Gold Compounds To Their Metallic Form

Australian scientists have found that the bacterium Cupriavidus metallidurans catalyzes the biomineralization of gold by transforming toxic gold compounds to their metallic form using active cellular mechanism.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 12:00 pm

'Blue Stonehenge' Discovered By UK Archaeologists

Archaeologists have released an artist's impression of what a second stone circle found a mile from Stonehenge might have looked like. The drawing shows the sensational discovery of "Blue Stonehenge" by a team led by UK archaeologists on the West bank of the River Avon last month.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 12:00 pm

Being Overweight Super-sizes Both Risk And Consequences Of Sleep-disordered Breathing

Overweight individuals are not just at greater risk of having sleep-disordered-breathing, they are also likely to suffer greater consequences, according to new research.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 9:00 am

Major Improvements Made In Engineering Heart Repair Patches From Stem Cells

Researchers have engineered more viable heart repair patches from mixed stem cells. The patches beat spontaneously, can be electronically paced and have pre-formed blood vessels that connect to a rodent's heart circulation.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 9:00 am

New Mesozoic Mammal: Discovery Illuminates Mammalian Ear Evolution While Dinosaurs Ruled

An international team of paleontologists has discovered a new species of mammal that lived in China's Liaoning Province 123 million years ago. This remarkably well preserved fossil offers important insight into how the mammalian middle ear evolved. Such exquisite dinosaur-age mammals provide evidence of how developmental mechanisms have impacted the evolution of the earliest mammals.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 9:00 am

Owners Should Count Calories For Obese Pets, Consider Several Factors For Good Health

You might watch your daily calorie intake or glance over nutritional information on food packages, but do you do the same for your pet? Veterinarians say there are several guidelines to follow when feeding your pet to ensure that it maintains good health.
Source: ScienceDaily: Latest Science News | 9 Oct 2009 | 9:00 am

US spacecraft set for Moon crash

Nasa is set to crash two unmanned spacecraft into the Moon in a bid to detect the presence of water-ice.
Source: BBC News | Science & Environment | UK Edition | 9 Oct 2009 | 4:22 am

NASA to moon: Get ready because here we come (AP)

This artist's rendering provided by NASA via Brown University shows the Centaur upper stage rocket separating from its shepherding spacecraft on a trajectory toward the moon. On Friday, Oct. 9, 2009, NASA will crash the Lunar Crater Observation and Sensing Satellite, or LCROSS, into a crater on the moon’s south pole to search for evidence of water ice. (AP Photo/NASA)AP - Two NASA spacecraft are barreling toward the moon at twice the speed of a bullet, about to crash into a lunar crater in a search for ice.



Source: Yahoo! News: Science News | 9 Oct 2009 | 4:18 am

Ask AP: Natural gas, how NFL players are paid (AP)

FILE - This Sept. 11, 2009 shows a U.S. Coast Guard boat during a training exercise in the Potomac River in Washington. A reader-submitted question about the number active-duty Coast Guard volunteer is being answered as part of an Associated Press Q&A column called 'Ask AP.'  (AP Photo/Haraz N. Ghanbari, File)AP - One natural resource the United States has a lot of is natural gas. So why not just start using it in place of oil, to reduce the nation's dependence on imported energy?



Source: Yahoo! News: Science News | 9 Oct 2009 | 4:12 am

Israelis bring green power to West Bank village (AP)

A Palestinian woman carries a bucket on her head as she passes a solar panel, in the West Bank village of Susya near Hebron, Wednesday, Oct. 7, 2009. Residents of a West Bank village bereft of electricity have been lifted out of the dark ages by an unlikely aid: a group of Israelis who installed solar panels and wind turbines to illuminate their makeshift homes. (AP Photo/Nasser Shiyoukhi)AP - Residents of a West Bank village with no electricity have been helped out of the darkness by unlikely benefactors — a group of Israelis who installed solar panels and wind turbines to illuminate the Palestinians' makeshift homes.



Source: Yahoo! News: Science News | 9 Oct 2009 | 3:58 am

Energy sector must invest massively: watchdog (AFP)

The country's energy regulator said that investment of up to 200 billion pounds in power plants and other infrastructure is needed over the next decade to secure energy supplies and meet climate change targets.(AFP/File/Shaun Curry)AFP - The country's energy regulator said Friday that investment of up to 200 billion pounds in power plants and other infrastructure is needed over the next decade to secure energy supplies and meet climate change targets.



Source: Yahoo! News: Science News | 9 Oct 2009 | 3:52 am

The nation's weather (AP)

AP - A cold front is expected to sweep across the country on Friday bringing more heavy rain and thunderstorms to the Southern Plains and East.
Source: Yahoo! News: Science News | 9 Oct 2009 | 3:29 am

ME virus discovery raises hopes

US research suggests a single virus may play a role in the development of chronic fatigue syndrome.
Source: BBC News | Science & Environment | UK Edition | 9 Oct 2009 | 3:11 am

In search of water NASA prepares to bomb the moon (AFP)

NASA would make an explosive return to the moon when it sends a satellite and a rocket booster crashing into a lunar crater to look for water.(AFP/NASA/File/Ho)AFP - NASA would make an explosive return to the moon Friday when it sends a satellite and a rocket booster crashing into a lunar crater to look for water.



Source: Yahoo! News: Science News | 9 Oct 2009 | 2:57 am

Glacier technology feels the heat

British technology designed to measure glaciers may hold the secret to predicting landslides, scientists believe.
Source: BBC News | Science & Environment | UK Edition | 9 Oct 2009 | 2:49 am

Landslide deaths lift Philippine storm toll past 540 (AFP)

Aerial photo shows flooded rice and corn fields in the northern Philippines. A series of landslides triggered by heavy rains killed at least 181 people in mountainous provinces of the northern Philippines.(AFP/File/Mike F. Alquinto)AFP - The death toll from two weeks of unprecedented storms across the northern Philippines soared past 540 on Friday after landslides consumed homes and neck-deep floods inundated towns.



Source: Yahoo! News: Science News | 9 Oct 2009 | 2:39 am

UN talks to end without deal on crucial issues (AP)

u.s.=AP - U.N. climate talks ended in a whimper Friday without progress on the pressing issues of emission cuts for wealthy nations or financing for the developing ones, both of which are crucial to reaching a global warming pact.



Source: Yahoo! News: Science News | 9 Oct 2009 | 2:34 am

Woolly thinking

Eco-living through carbon-neutral design
Source: BBC News | Science & Environment | UK Edition | 9 Oct 2009 | 12:52 am

Generation 100

Can you really trust long life expectancy predictions?
Source: BBC News | Science & Environment | UK Edition | 8 Oct 2009 | 11:57 pm

Stem Cell Research Offers Hope for Colon Cancer Vaccine (HealthDay)

HealthDay - WEDNESDAY, Oct. 7 (HealthDay News) -- Human stem cells may provide a means of creating a vaccine against colon cancer and other types of cancers, say American and Chinese scientists.
Source: Yahoo! News: Science News | 8 Oct 2009 | 9:49 pm

New Technology Shows Human Genome in 3-D (HealthDay)

HealthDay - THURSDAY, Oct. 8 (HealthDay News) -- The 3-D structure of the human genome has been deciphered by U.S. researchers, an achievement that improves understanding of genomic function and reveals how two meters of DNA can be packed into each human cell.
Source: Yahoo! News: Science News | 8 Oct 2009 | 9:49 pm

Study isolates virus in chronic fatigue sufferers

WASHINGTON (Reuters) - A virus linked to prostate cancer also appears to play a role in chronic fatigue syndrome, according to research that could lead to the first drug treatments for a mysterious disorder that affects 17 million people worldwide.

Source: Reuters: Science News | 8 Oct 2009 | 6:50 pm

'First Bird' Not Very Bird-Like

Tiny bone chips from a primitive bird suggest it grew more like a dinosaur.
Source: Livescience.com | 8 Oct 2009 | 6:00 pm

Crash Into the Moon With LCROSS Friday Morning

lcross_impact

Tomorrow morning you’ll have a rare opportunity to experience a live moon crash. At 7:31 a.m. EDT, NASA’s LCROSS satellite will send a rocket hurtling toward the moon at a whopping 1.55 miles per second, and a camera mounted on the spacecraft will send live footage back to Earth. Four minutes later, the entire satellite will smack into the moon, generating a giant plume of debris that should be visible from our planet with an amateur telescope.

To find out how and where to watch the carnage, check out the posts by our friends at GeekDad:

  • Ways to See LCROSS Crash on Friday Morning
  • Moon Shot Part Deux: Even More Ways of Observing the LCROSS Impact …
  • Image: Northrup Grumman

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    Follow us on Twitter @wiredscience, and on Facebook.



    Source: Wired: Wired Science | 8 Oct 2009 | 5:36 pm

    The Periodic Table by Primo Levi

    As a survivor of Auschwitz, Levi offers fiction, non-fiction, allegory and reality wrapped in a metaphor of chemistry to brings us a layered vision of his world. Tim Radford wonders if The Periodic Table can be called science writing, but has no doubt about its merit

    It was awarded – in a very informal vote – the title of the best science book ever written, but what makes it a science book at all? Levi was a working chemist, but the title is a metaphor and even this figure of speech is sometimes a little strained to comply with the book's scheme.

    Some of it is personal memoir, and chapter headings such as Argon, and Iron, seem barely justified by the reflections that follow. Some stories are overtly fiction, which is surely the antithesis of science writing. One or two are attempts to address the process of industrial science from, so to speak, the floor: Sulphur is a compelling account of a wartime factory hand's hours on the night shift, but what is he making, and why does he need such temperatures, such vacuum readings?

    Some of it is about etymology, about the nature of words and their casual links with the elements around us. And some of it is urgent, cruel, personal history: the story of a young man born into a Jewish family, educated in Fascist Italy, all but destroyed in Auschwitz. The chemistry is important, but often incidental. And finally, it is not Levi's greatest work. For that, go to If This Is A Man, and The Truce.

    And yet, on the fourth or fifth reading in the 24 years since UK publication, The Periodic Table still seems to me to be the nearest match to the ideal science book. At some point – for me it was page 33 of the original Michael Joseph edition – the reader begins to understand that chemistry is not a "subject", not an arcane and sometimes bewildering intellectual scaffolding laboriously erected to frame reality: it is reality. Chemistry is what happens when we breathe, when we touch, when we react, and even our behaviour with others is chemistry at some greater level.

    This realisation (once again, for me) came as Levi describes the laboratory preparation of zinc sulphate. He discovers that "the so tender and delicate zinc, so yielding to acid which gulps it down in a single mouthful, behaves, however, in a very different fashion when it is very pure …" The reaction requires impurity, a touch of strangeness, a drop of copper sulphate in the diluted sulphuric acid, or it won't work. He of course, is a Jew among Mussolini's Blackshirts, and draws a philosophical lesson: purity protects; but impurities give rise to change, and generate life. "Dissension, diversity, the grain of salt and mustard are needed: Fascism does not want them, forbids them, and that is why you are not a Fascist, it wants everybody to be the same, and you are not."

    Tropes such as this are a writer's business, but right through the book, sometimes without comment, Levi offers parallels between the reactions in a test tube and the things that happen in the world at large: there is another beautiful one when he cannot find the sodium necessary to purify and dehumidify the benzene he wants to distil, and so instead uses its twin in the periodic table, potassium, and nearly blows up the laboratory. From it he concludes that one dare not trust the almost-the-same, the practically identical. "The differences can be small, but they lead to radically different consequences, like a railroad's switchpoints; the chemist's trade consists in good part in being aware of those differences, knowing them close up, and foreseeing their effects. And not only the chemist's trade."

    It is of course, that last, understated sentence that does the trick. Levi never claims too much; never protests too much. The narratives drive home the lessons, and such stories they are! They include his clandestine, and somewhat pointless employment – recruited, against all fascist laws by the Italian army – in an asbestos mine; the way a few rods of cerium became a currency that secured his survival in the concentration camp; the mad post-war attempt to try to synthesise, from chicken shit, the mysterious factor that made American lipstick so glossily kiss-proof; and an eerie moment in the business correspondence with a German supplier about the quality of a batch of vanadium naphthenate, when Levi realises that he is dealing with the man who headed the Auschwitz laboratory in which he had been a slave labourer.

    You cannot, in a book that invokes Auschwitz, fascism and the reconstruction of a devastated continent, disentangle the human drama from the science, but each time I read The Periodic Table I also discover myself marvelling at the excitement locked in obdurate and mundane matter and the chemist's attempts to transmute it into something new, and fresh, and potent: whoever would have thought that tin could preserve such secrets, that industrial varnish could be so thrilling?

    I have four anthologies of science writing on my shelves – by Bernard Dixon, Timothy Ferris, Richard Dawkins and John Carey – and a selection from The Periodic Table is to be found in every one of them. I do not claim to be original in proselytising for Primo Levi. But The Periodic Table really does seem to me to be a very special thing, an interaction of profound knowledge and terrible experience and transcendent literary skill, catalysed by another, more difficult to define ingredient, which for want of a better word, might be called goodness. If you were looking for a good book, a really good book in every sense, this is it.

    Next month, something completely different. The late Stephen Jay Gould was one of the great science writers and he also more or less reinvented that wonderful, loquacious Victorian form, the essay. But I am looking forward to re-reading his sustained and angry attack on eugenics: The Mismeasure of Man.


    guardian.co.uk © Guardian News & Media Limited 2009 | Use of this content is subject to our Terms & Conditions | More Feeds


    Source: Science news, comment and analysis | guardian.co.uk | 8 Oct 2009 | 5:05 pm

    "Cirque" founder hosts space show for Earth's water

    LOS ANGELES (Reuters) - Guy Laliberte, the Canadian billionaire circus entrepreneur, flew into space with a clown nose and an idea that was literally out of this world.

    Source: Reuters: Science News | 8 Oct 2009 | 4:19 pm

    Your Bug-Coated Windshield Is Lousy With Genomes

    1271582892_0510d1f806_b

    That disgusting layer of bug guts plastered across your bumper after a road trip could also be a great way to analyze the biodiversity of where you’ve been.

    After a long-distance drive to a conference yielded a tremendous number of squashed bugs on his bumper, genomics researcher Anton Nekrutenko of Pennsylvania State University decided to try an experiment: Why not apply the tools of metagenomics, which is the study of DNA taken directly from an environmental sample, to the collection of insects decorating his car?

    “How many species inhabit our immediate surroundings?” wrote Nekrutenko and colleagues in a paper published Thursday in Genome Research. “A straightforward collection technique suitable for answering this question is known to anyone who has ever driven a car at highway speeds.”

    By sequencing DNA taken from the bug splatter generated by two different car trips, one from Pennsylvania to Connecticut and the other from Maine to New Brunswick, Canada, the researchers discovered significant differences in insect diversity between the two regions.

    bumper_car1In addition to proving that bug carnage can provide valuable information about biodiversity, the experiment served as proof-of-principle for a new kind of metagenomic analsyis. Until now, metagenomics had been used primarily to study mixed samples of bacteria, such as the microbes that inhabit the human gut or live on the surface of our skin. But scientists are increasingly interested in applying the same shotgun analysis of genetic material to answer questions about higher organisms.

    For instance, researchers have debated for decades just how many different kinds of insects are out there, with estimates ranging from 10 million to 30 million. Of those, only a few hundred thousand have been cataloged by biologists. But analysis of insect diversity from environmental DNA samples is incredibly complex, and the researchers say our current computational tools aren’t quite up to the task.

    “It’s somewhat easier with bacteria because normally bacteria have small genomes, and their genomes are packed with genes that produce proteins,” Nekrutenko said. Higher organisms are more complicated because they tend to have larger genomes and more “junk” DNA that doesn’t code for proteins. To handle analysis of the massive amounts of data necessary to screen even a simple collection, like bugs scraped from a car, the group had to create new tools.

    “One of our main goals was technology development,” Nekrutenko said. “In general, life sciences are becoming kind of like physics, very data-driven, but most biologists are not trained in data-driven research.” Along with colleagues from the University of California, San Diego and Emory University, Nekrutenko’s group developed a straightforward, web-based program called Galaxy that walks scientists through the steps of metagenomic analysis, from obtaining raw sequencing data to drawing up an evolutionary tree.

    Some biologists who have already started using Galaxy give it rave reviews. “My lab would be lost without it,” said biologist Ross Hardison of Pennsylvania State University, who has collaborated with Nekrutenko but was not involved in this research. “We are dependent on Galaxy for a very large fraction of the analyses we do.”

    Even more importantly, Nekrutenko said, Galaxy allows researchers to publish their entire dataset and methods so that other researchers can reproduce their results. “Metagenomics is kind of a parameter-dependent science,” Nekrutenko said. “You run certain tools, and they have dials, and depending how you set these dials you can get completely different results. Through our system, you can see exactly how we set these dials.”

    That means other researchers can repeat Nekrutenko’s analysis and see if they get the same results. For instance, someone might want to double-check a particularly bizarre feature of the data: In addition to finding plenty of insect and bacterial DNA, the group uncovered genetic material from the genus Homo.

    Nekrutenko said the unexpected result probably represents an artifact: Because current databases of eukaryotic DNA sequences are dominated by the human genome, spurious human results are likely to pop up. “Precise species ID from mixed samples like this is very, very challenging,” he said. “We have sequences that map to human DNA, even though I’m pretty sure we didn’t kill anybody.”

    Image 1: Flickr/John Beales. Image 2: A photograph of Nekrutenko’s bumper after one of the bug collection trials/Anton Nekrutenko.

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    Source: Wired: Wired Science | 8 Oct 2009 | 3:53 pm

    Europa, Jupiter's Moon, Could Support Complex Life

    Europa may have enough oxygen to support complex, animal-like organisms.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 3:30 pm

    Direction of NASA’s Future at an Impasse

    ares-i

    The committee charged with rethinking American human spaceflight is done thinking, but it’s still unclear what the future of NASA’s astronaut corps might be, and some nagging issues have yet to be resolved.

    The U.S. Human Space Flight Plans Committee — known informally as the Augustine commission, after its head Norm Augustine, former CEO of Lockheed Martin — held its last teleconference today. The ball, or hot potato, will soon be in the Obama administration’s court when the group formally presents its alternatives to the Office for Science and Technology Policy.

    “We did not rate the overall options because, first of all, we were not asked to do that — and doing it would have required that we apply some sort of judgment as to what the relative weighting of those factors should be,” Augustine said.

    Even in its waning days, though, some controversies remain. The final meeting revealed some internal disputes within the group on how to “score” the alternative plans. A particularly sticky issue is the safety of the Ares I rocket, a key component of the current Constellation program.

    The safety risk the panel assigned to the various human spaceflight options was based largely on the destination of the missions — to low-Earth orbit, the moon or elsewhere.

    The specific vehicles and systems involved in the missions were not a significant factor, said Ed Crawley, an MIT professor and committee member, in introducing the meeting.

    Still, some members, notably Bohdan Bejmuk, chair of the Constellation program Standing Review Board, argued that the Ares I should get a higher safety rating than its competitors.

    “I completely disagree with that assessment,” shot back Jeff Greason, CEO of XCOR Aerospace and vice-chair of Personal Spaceflight Federation.

    Other committee members, notably Augustine himself, tried to find common ground between the panel members, but the dispute clearly remains.

    “Different partisans of different systems have arguments for why their systems should be exempt from the lessons of history,” Greason said, before noting that probabilistic risk assessments based on the architecture of a particular space machine don’t capture 90 percent of the accidents that have actually occurred.

    Still, Bejmuk stuck to his guns, arguing multiple times that the Ares I was intrinsically safer than the alternatives.

    “The program of record has a simpler rocket and we’re not giving it credit,” he contended.

    Disagreement among these experts won’t make decision-making any easier for John Holdren, Obama’s top science adviser, who created the panel. The panel’s summary report, released in September, a few weeks later than scheduled, seemed to raise as many question as it answered. During congressional hearings, Augustine faced heated questions from several House members who attacked the meaning and methodology of the committee’s work.

    “Instead of focusing on how to strengthen the exploration program in which we have invested so much time and treasure,” Rep. Gabrielle Giffords (D-Arizona), chair of the space subcommittee, railed, “they gave only glancing attention to Constellation — even referring to it in the past tense in their summary report and instead spent the bulk of their time crafting alternative options that do little to illuminate the choices confronting Congress and the White House.”

    Many questioned whether the Augustine commission had given enough attention to the safety of astronauts. Several others questioned the emphasis that the Augustine committee placed on working with commercial entities.

    Augustine got a kinder, almost bored reception in the Senate, but it seems clear that any plan the Obama administration may entertain to scrap the Bush-era Constellation program will face fierce criticism.

    Image: Ares I test fires.
    NASA

    See Also:

    WiSci 2.0: Alexis Madrigal’s Twitter, Google Reader feed, and green tech history research site; Wired Science on Twitter and Facebook.



    Source: Wired: Wired Science | 8 Oct 2009 | 3:25 pm

    Prehistoric Mammal Hints at Ear's Evolution

    A 123-million-year-old chipmunk-sized mammal may explain how human hearing evolved.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 2:20 pm

    The Human Genome in 3 Dimensions

    genome_folding

    By breaking the human genome into millions of pieces and reverse-engineering their arrangement, researchers have produced the highest-resolution picture ever of the genome’s three-dimensional structure.

    The picture is one of mind-blowing fractal glory, and the technique could help scientists investigate how the very shape of the genome, and not just its DNA content, affects human development and disease.

    “It’s become clear that the spatial organization of chromosomes is critical for regulating the genome,” said study co-author Job Dekker, a molecular biologist at the University of Massachusetts Medical School. “This opens up new aspects of gene regulation that weren’t open to investigation before. It’s going to lead to a lot of new questions.”

    As depicted in basic biology textbooks and the public imagination, the human genome is packaged in bundles of DNA and protein on 23 chromosomes, arrayed in a neatly X-shaped form inside each cell nucleus. But that’s only true during the fleeting few moments when cells are poised to divide. The rest of the time, those chromosomes exist in a dense and ever-shifting clump. Of course their constituent DNA strings are clumped, too: If the genome could be laid out end-to-end, it’d be six feet long.

    For decades, some cell biologists suspected that the genome’s compression wasn’t just an efficient storage mechanism, but linked to the very function and interaction of its genes. But this wasn’t easy to study: Sequencing the genome destroys its shape, and electron microscopes can barely penetrate its active surface. Though its constituent parts are known, the genome’s true shape has been a mystery.

    In April, a paper published in the Proceedings of the National Academy of Sciences linked patterns of gene activation to their physical proximity on chromosomes. It still provided the most persuasive evidence to date that genome shape matters, even though the researchers’ chromosome map was relatively low-resolution. The topography described in the latest research, published Thursday in Science, is far more detailed.

    “It’s going to change the way that people study chromosomes. It will open up the black box. We didn’t know the internal organization. Now we can look at it in high resolution, try to link that structure to the activity of genes, and see how that structure changes in cells and over time,” said Dekker.

    To determine genome structure without being able to directly see it, the researchers first soaked cell nuclei in formaldehyde, which interacts with DNA like glue. The formaldehyde stuck together genes that are distant from each other in linear genomic sequences, but adjacent to each other in actual three-dimensional genomic space.

    The researchers then added a chemical that dissolved the gene-by-gene linear sequence bonds, but left the formaldehyde links intact. The result was a pool of paired genes, something like a frozen ball of noodles that had been sliced into a million fragmentary layers and mixed.

    By studying the pairs, the researchers could tell which genes had been near each other in the original genome. With the aid of software that cross-referenced the gene pairs with their known sequences on the genome, they assembled a digital sculpture of the genome. And what a marvelous sculpture it is.

    “There’s no knots. It’s totally unentangled. It’s like an incredibly dense noodle ball, but you can pull out some of the noodles and put them back in, without disturbing the structure at all,” said Harvard University computational biologist Erez Lieberman-Aiden, also a study co-author.

    In mathematical terms, the pieces of the genome are folded into something similar to a Hilbert curve, one of a family of shapes that can fill a two-dimensional space without ever overlapping — and then do the same trick in three dimensions.

    How evolution arrived at this solution to the challenge of genome storage is unknown. It might be an intrinsic property of chromatin, the DNA-and-protein mix from which chromosomes are made. But whatever the origin, it’s more than mathematically elegant. The researchers also found that chromosomes have two regions, one for active genes and another for inactive genes, and the unentangled curvatures allow genes to be moved easily between them.

    Lieberman-Aiden likened the configuration to the compressed rows of mechanized bookshelves found in large libraries. “They’re like stacks, side-by-side and on top of each other, with no space between them. And when the genome wants to use a bunch of genes, it opens up the stack. But not only does it open the stack, it moves it to a new section of the library,” he said.

    The segregation of active and inactive genes adds to evidence that genome structure affects gene function.

    “It’s a great description of the structure of the nucleus, and if you put that on top of what we did, it forms the big picture,” said Steven Kosak, a Northwestern University cell biologist and co-author of the April PNAS paper that linked rough outlines of chromosome arrangement to gene activation. Whereas that study only looked at a few chromosomes, the Science paper “looks at fine resolution over the whole genome,” said Kosak.

    “Now you can produce these genome maps, and superimpose them with genome-wide analyses of gene expression. You can really start asking how changes in spatial organization relate to changes in genes turning on and off,” said Tom Misteli, a National Cancer Institute cell biologist who studies how glitches in chromosome structure may turn cells cancerous. Neither Misteli nor Kosak were involved in the Science study.

    Connecting genome shape to gene function could also help explain the connection between genes and disease, which remain largely unexplained by traditional, sequence-focused genomics.

    “It’s perfectly reasonable and almost inevitable that the 3-D structure of DNA is going to influence how it functions,” said Teri Manolio, director of the National Human Genome Research Institute’s Office of Population Genomics.

    Researchers also want to study how genome shape is altered. That appears to happen constantly during the transition from stem cell to adult cell, and then during cell function.

    “How much variation is there in structure across cell types? What controls it? Exactly how important is it? We don’t know,” said Dekker. “This is a new area of science.”

    Image: From Science, a two-dimensional Hilbert curve, and the three-dimensional shape of a genome.

    See Also:

    Citation: “Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome.” Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, MarkGroudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, Job Dekker. Science, Vol. 326 No. 5950, October 9, 2009.

    Brandon Keim’s Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecosystem and planetary tipping points.



    Source: Wired: Wired Science | 8 Oct 2009 | 1:16 pm

    Dead Zones Doubling Every Decade

    Scientists say dead zones are on the rise.
    Source: Livescience.com | 8 Oct 2009 | 1:05 pm

    Royal blood disorder identified

    DNA analysis reveals the identity of the "cursed blood" disorder that afflicted the British Royal Family.
    Source: BBC News | Science & Environment | UK Edition | 8 Oct 2009 | 12:26 pm

    BIG PIC: Asteroid ID'd as Baby Planet

    One of the largest asteroids in the asteroid belt gets protoplanet status after new analysis.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 12:20 pm

    As Reactions to Threats Fade, Fear Does Too

    Emotions make us fear newer threats more than old ones, according to research.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 11:30 am

    Tiny 'nuclear batteries' unveiled

    A team of researchers in the US has demonstrated a tiny battery powered by the decay of radioactive isotopes.
    Source: BBC News | Science & Environment | UK Edition | 8 Oct 2009 | 11:15 am

    Even Modest Exercise Boosts Self-Image

    Those who hit the gym are likely to feel better about their bodies.
    Source: Livescience.com | 8 Oct 2009 | 11:06 am

    The Pill May Alter Sex Partner Preferences

    A study suggests that being on birth control may influence the type of men women pick.
    Source: Livescience.com | 8 Oct 2009 | 10:50 am

    Pigs Use Mirrors to Find Hidden Food

    428341583_402dfb2615_o

    In just five hours, an average farm pig can learn how to interpret an image in the mirror and use it to find hidden food.

    Scientists consider the ability to use a mirror a sign of complex cognitive processing and an indication of a certain level of awareness. In addition to humans and some primates, dolphins, elephants, magpies and a famous African grey parrot named Alex have all been known to retrieve objects or remove marks on their body using a mirror. Now it looks like pigs should be added to the list of clever critters that can master a mirror: After spending five hours with a mirror in their pen, seven out of eight pigs could use the reflection to find a hidden bowl of grub.

    “This is the first demonstration of the ability of pigs to use mirrors,” animal behavior expert Donald Broom of the University of Cambridge wrote in an e-mail. “Finding sophisticated learning and awareness in animals can alter the way that people think about the species and may result in better welfare in the long run.” Broom co-authored the paper published this month in Animal Behaviour.

    Like most animals, the pigs were immediately curious when researchers placed the shiny, reflective object in their pen. They approached the mirror until they bumped into it with their snout, and then checked to see what was behind the mirror. The pigs spent an average of 20 minutes gazing at their reflection, often turning in different directions to inspect themselves from several angles.

    “These kind of movements suggest that the pigs were correlating the movements of their body with the visual stimulus they were receiving from the mirror, and so learning the contingency between the two,” biologist Louise Barrett of the University of Liverpool wrote in a commentary about the paper, also published this month in Animal Behaviour.

    After five hours with a mirror, the pigs were placed in a new test area that contained a food bowl hidden behind a barrier. Although the pigs could see the reflection of the bowl in the mirror, they couldn’t see the food directly. A fan above the bowl circulated the scent of food around the room, prohibiting the pigs from smelling their way to the treat.

    Seven out of eight of the pigs with previous mirror experience spotted the reflection of the food bowl and correctly interpreted its location: Instead of searching for the food in its apparent position behind the mirror, the pigs headed around the barrier and straight for the true location of the bowl. When the researchers tested pigs with no prior mirror exposure, however, nine out of 11 of them became confused, searching behind the mirror for the food.

    “These results suggest not only that pigs learn the contingency between their own movements and their image in the mirror,” Barrett wrote, “but that their knowledge incorporates the layout of the environment as well, so that they can locate objects in space.”

    The researchers say their experiment is more than a nifty trick: The fact that pigs can learn to use a mirror means they are capable of a type of awareness called assessment awareness, which means they can understand the significance of a situation in relation to themselves, over a short period of time. In this case, the pigs remembered how their own movements appeared in the mirror, and were able to apply that knowledge to a separate situation involving a hidden food bowl.

    “Having a sense of self and using it is a form of assessment awareness,” Broom wrote. Although the mirror experiment doesn’t directly prove that pigs have a sense of self, the researchers suggest that given how quickly the pigs learn to recognize their own movements in a mirror, they may have some degree of self-awareness. “We have no conclusive evidence of a sense of self,” Broom wrote, “but you might well conclude that it is likely from our results.”

    Other mirror tests have been used to more directly examine an animal’s sense of self — if researchers apply a yellow mark to the black feathers of a magpie, for instance, the bird will use a mirror to clean itself off. Unfortunately, Broom says the mark experiments just don’t work on pigs: Pigs are so accustomed to being streaked with mud, they don’t much care if researchers apply extra marks on their bodies. “We have put marks on pigs,” Broom wrote. “They take little notice of them.”

    Combined with a host of other research studies demonstrating the keen intelligence of pigs, the researchers hope their study will lead to better treatment of the farm animals. “If an animal is clever,” Broom wrote, “it is less likely to be treated as if it is an object or a machine to produce food, and more likely to be considered as an individual of value in itself.”

    Image: Flickr/The Pug Father

    See Also:

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    Source: Wired: Wired Science | 8 Oct 2009 | 10:48 am

    Waste firm ban in cyanide probe

    A waste company is banned from discharging industrial effluent into sewers after a cyanide leak in the River Trent.
    Source: BBC News | Science & Environment | UK Edition | 8 Oct 2009 | 10:42 am

    Monkey Moms Act Like Human Moms

    The mother-child bond may have roots in other primates.
    Source: Livescience.com | 8 Oct 2009 | 10:09 am

    Monkey mothers 'coo' over babies

    The way that rhesus macaque mothers bond with their babies bears a remarkable resemblance to human behaviour.
    Source: BBC News | Science & Environment | UK Edition | 8 Oct 2009 | 10:06 am

    Dodging a bullet: how likely is this asteroid to collide with Earth?

    An asteroid once predicted to have a reasonable chance of striking Earth in 2036 is now far more likely to be a "near miss".
    Source: BBC News | Science & Environment | UK Edition | 8 Oct 2009 | 10:04 am

    'Whatever' Tops List of Most Annoying Words

    A recent poll of the most annoying words places the slacker term "whatever" on top.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 9:45 am

    Counting Elephants by Voice

    bai_01

    By putting microphones in the jungle, researchers are better able to perform the surprisingly tricky task of counting elephants.

    Sure, pachyderm polling doesn’t seem difficult. They’re not exactly hard to see. But covering hundreds of square miles, day after day, requires time, money and personnel — all of which are in short supply in the developing countries where elephants live.

    Enter the Elephant Listening Project at Cornell University. Using acoustic monitoring and analysis techniques originally developed for counting birds by song, it tracks elephants in the jungles of Central Africa.

    In a paper published in the September African Journal of Ecology, project researchers describe the calibration of their model at a Central African Republic site. First they personally observed forest clearings where elephants were known to gather, counting the animals they saw and the noises they made. The researchers then turned these observations into a framework for interpreting recordings made by microphones installed throughout the forest.

    The same approach “provides an opportunity to improve management and conservation of many acoustically active taxa whose populations are currently under-monitored,” wrote the researchers.

    In addition to being relatively inexpensive and geographically comprehensive, bioacoustic monitoring offers other advantages over traditional animal counts. It can give detailed ecological snapshots, counting anything that makes a noise.

    For the elephant counts, each monitor covered a square mile of ground, “a dramatic increase in coverage over dung survey transects.” In other words, it’s a lot easier to listen to elephants than gather their poop.

    Image: Elephant Listening Project

    Via the Conservation Maven.

    See Also:

    Citation: “Acoustic estimation of wildlife abundance: methodology for vocal mammals in forested habitats.” By Mya E. Thompson , Steven J. Schwager, Katharine B. Payne and Andrea K. Turkalo. African Journal of Ecology, Vol. 47 No. 3, September, 2009.

    Brandon Keim’s Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecosystem and planetary tipping points.



    Source: Wired: Wired Science | 8 Oct 2009 | 9:34 am

    BLOG: More South Pacific Quakes = Armageddon?

    A recent string of tremors may trigger much larger quakes in the future.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 8:30 am

    NASA Bombing Moon in Search of Water

    A 2.5-ton deadweight will be crashed into a lunar crater to see if it holds water.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 8:30 am

    Proposal Would Turn San Francisco Bridge into a City

    New idea may allow residents to live under the bridge in style.
    Source: Livescience.com | 8 Oct 2009 | 7:34 am

    BLOG: Could Zombieland Really Happen?

    Could an unknown virus really turn humans into zombies?
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 7:30 am

    BIG PIC: Black Holes Face Off

    In a few million years, in a galaxy far, far away, two black holes will collide.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 7:30 am

    AI Helps Doctors Diagnose Deadly Conditions

    Artificial intelligence programs help doctors diagnose heart infections and treat wounds.
    Source: Discovery News Top Stories : Discovery Channel | 8 Oct 2009 | 7:15 am

    Airline's green claim vanishes into Finnair

    Finland's national carrier blitzes Europe with plain stupid marketing strategy that amounts to eco-vandalism

    The national airline of Finland has a new marketing strategy. Finnair wants us to fly to Asia via Helsinki. It's a sensible business plan, I guess. There aren't so many Finns wanting to fly to Asia, so they encourage others to fly to Finland and join them on the long haul.

    The company is currently blitzing Europe cities such as London with posters claiming that flying Finnair to Asia is both quicker and "eco-smart".

    So is this greenwash?

    I took this up with Kati Ihamäki, who was last year appointed the company's vice-president for sustainable development "as part of [Finnair's] quest to become the airline of choice for environmentally conscious passengers in international travel".

    Her case is this. First, Helsinki is on a direct route to much of Asia from both Europe and North America. It may not look like it from most maps, but you'll see what she means if you check out a globe, or look at this Great Circle Mapper.

    Fair enough, but most direct routes to China, India and south-east Asia already fly over Finland. So why bother to land and take off again? Her answer is that breaking the journey means planes can carry less fuel.

    Most of the payload when a long-haul flight takes off is not passengers or cargo but fuel. It can be five times the "payload", so breaking the journey into smaller hops cuts the fuel load.

    But there is a catch. Planes use most fuel during take-off and getting to cruising altitude. Typically this process burns as much fuel as cruising for 700-800 kilometres. Taking off twice (say, once in London and once in Helsinki) will therefore burn up more fuel than taking off once.

    So there is a balance. And Ihamaki's case is that on those really long hauls to Asia — anything over 10 hours, she writes in a blog on the company site — the balance is in favour of a stopover.

    You can cut your emissions when flying from New York to New Delhi by 28% if you make a stop-off at Helsinki, Finnair claims (pdf).

    Others agree that stopovers are best on the longest journeys. When Britain's Royal Commission on Environmental Pollution investigated air travel (pdf) a few years ago, it found that the fuel burned "per passenger kilometre" was highest for short-haul flights (where most of the journey is fuel-intensive takeoff and climbing) and for very long-haul flights (through carrying so much fuel).

    But the commission found a modest "sweet spot" in the middle. At around 4,300 kilometres (2,672 miles), emissions were as much as 10% less than for very long or short flights.

    So does that make Finnair right? Not quite.

    For one thing, a flight from London (or Frankfurt, or Amsterdam) to Helsinki is less than half the "sweet spot" distance.

    By my calculation, based on the Royal Commission's findings, Finnair is right that if you are flying from London to Hong Kong it is better to stop over at Helsinki than go direct. But Finnair's scientists agreed with me that for a journey from London to Beijing it makes virtually no difference, and for Delhi or Mumbai you would emit fewer greenhouse gas emissions on a direct flight.

    So Finnair have their science right. But their marketing is hype. It is by no means always "eco-smart" to fly to Asia via Helsinki, because the emissions from the short hop to Finland's capital often outweigh the benefits on the rest of the journey.

    Worse still, a lot of the stop-over flights Finnair offers from Europe to Asia via Helsinki are plain stupid. Its schedules advertise crazy dog-leg journeys like Moscow to Bangkok via Helsinki. That is: flying west to Helsinki before taking a flight east that is even longer than going direct from Moscow. Istanbul to Bangkok via Helsinki is equally crazy. But those "eco-smart" guys are desperate to sell you a ticket.

    Finnair has opened a debate. In the coming years, as the airline business struggles to come to terms with internationally imposed limits on emissions, there will be a lot of new thinking: about taking more direct routes; reducing those irritating and fuel-burning holding circles before landing; cutting out super-long haul.

    All that is good. But Finnair's blanket claim that flying via Helsinki is eco-smart does not hold water. It is a marketing ruse, based on cherry-picking data, to help fill more planes to Asia. It is, for many journeys, greenwash.

    And encouraging us to think that it can be "eco-smart" to fly to Asia at all is an act of eco-vandalism.

    A cynic would say the best eco-news from Finnair this year is that collapsing demand has forced it to cancel 14% of its flights. Now that really is eco-smart.


    guardian.co.uk © Guardian News & Media Limited 2009 | Use of this content is subject to our Terms & Conditions | More Feeds


    Source: Science news, comment and analysis | guardian.co.uk | 8 Oct 2009 | 5:52 am

    Peak oil could hit soon – report

    A new report says worldwide production of conventionally extracted oil could peak in the next decade

    There is a "significant risk" that global oil production could begin to decline in the next decade, researchers said today.

    A report by the UK Energy Research Council (UKERC) said worldwide production of conventionally extracted oil could "peak" and go into terminal decline before 2020 – but that the government was not facing up to the risk.

    Falls in production will lead to higher and more volatile prices, and could encourage investment in even more polluting fossil fuels, such as tar sands, which "need to stay in the ground" to avoid dangerous climate change as a result of carbon emissions, the researchers said.

    The new report said there was too much geological, political and economic uncertainty to predict an exact date for peak oil, which would not lead to a sudden decline but a "bumpy plateau" with a downward trend in extraction.

    But Steve Sorrell, chief author of the report, said while those who forecasted an imminent decline had underestimated oil reserves, more positive forecasts suggesting oil production will not peak before 2030 were "at best optimistic and at worst implausible".

    The world has used less than half of the planet's conventionally extracted oil, but the remaining resources will be more difficult and expensive to get out of the ground, slowing production and increasing prices of crude.

    With exploitation of the world's reserves running at more than 80m barrels a day, even major new discoveries such as the oil fields recently found in the Gulf of Mexico by BP would only delay a peak by a few days or weeks, the report said.

    Robert Gross of UKERC said: "The age of easy and cheap oil is coming to an end. It doesn't suddenly come to an end; obviously it's a gradual change. But we're moving away from easy and cheap oil to increasingly difficult and expensive oil."

    The public should expect to see more higher and more volatile petrol costs in the future, with long-distance travel becoming pricier.

    Britons should invest in the most energy-efficient vehicles and put pressure on the government to take the issue seriously, the researchers urged. With long time-scales and large investment needed to move away from a reliance on crude oil – particularly in the transport sector, which uses the lion's share of fossil fuel – the report said governments needed to take action now.

    Sorrell said the UK government had no contingency plans for oil peaking before 2020, but officials needed to increase and speed up measures already being taken to cut climate emissions, such as improving vehicle fuel efficiency, shifting to electric cars and investing more in public transport.

    Though high oil prices could encourage investment in renewables and technological changes, they could also do the same for more polluting and energy-intensive forms of oil. These include tar sands, where extraction of fuel becomes viable when the oil price hits around $70/barrel – its current level – and converting coal to a liquid, which requires a great deal of energy.

    "Most of these unconventional resources need to stay in the ground, but [there are] such strong incentives to exploit them," he said.

    The consequences in terms of carbon emissions of unconventional sources of oil could be "catastrophic", Gross said.

    "The danger is, high oil prices push us into high carbon resources just as much as they might help push us towards renewables. The challenge for policymakers is to make sure, on a global scale, that that isn't the response to more difficult and expensive oil."

    A spokesman for the Energy and Climate Change Department said: "Already, our climate change, energy efficiency and energy security policies outlined in the UK low carbon transition plan are not only reducing the UK's carbon emissions, but are consistent with the need to reduce our use of fossil fuels.

    "This will help to ease demand for oil in the UK and internationally. In addition, the UK government is investing and supporting research on renewable and clean transport technologies – which is the UK sector that consumes most fossil fuels."


    guardian.co.uk © Guardian News & Media Limited 2009 | Use of this content is subject to our Terms & Conditions | More Feeds


    Source: Science news, comment and analysis | guardian.co.uk | 8 Oct 2009 | 4:16 am